Team:ZJUT-China/Model
Team:ZJUT-China
Abstract
In order to make sure that our system could be common used by the researchers who want to clean the ARG after experiments, we developed a model to Calculate the point when all ARG are cleaned and the bacteria suicide. We got test data of our parts and then built rate equations. And next we used those rate equations to simulate how our system work and tried to find a better ratio of the vector’s copy number.
System modeling Var1.0
d[cut off]/dt=kf*[sg]*[cas9]*[ARG]/(km+[ARG])
Result
This is the result we got by the ODE model of the light-controlled ARG cutting system ver1.0
System modeling Ver3.0
This presents an issue for researchers and factors who wish to make use of our system of the ARG killing parts in a more complex environment. In order to address this issue, we decided to develop a mathematical model of how light signal effects influence the time of cutting off all ARGs and bacteria's suicide induced by our ARG killing system.
In the light-controlled ARG cutting system ver3.0 we want to add 3 repressors, one more sgRNA, and a lysin gene to make our cells can cut off all the ARGs and then suicide in chronological order which is designed.
d[degrade_r1]/t=vm*[repressor_1]/([repressor_1]+km)
d[express_r2]/t=kf*[vector_2]
d[degrade_r2]/t=vm*[repressor_2]/([repressor_2]+km)
d[express_r3]/t=kf*[vector_1]
d[degrade_r3]/t=vm*[repressor_3]/([repressor_3]+km)
d[express_cas]/t=kf*[vector_1]*(vm-[repressor_1])
d[express_sg1]/t=0
d[express_sg2]/t=kf*[vector_2]*(vm-[repressor_2])
d[express_ly]/t=kf*[chromosome]*(vm-[repressor_3])
d[cut off_1]/t=kf*[ARG_1]*[sg_1]*[cas9]/(km+[ARG_1])
d[cut off_2]/t=kf*[ARG_2]*[sg_2]*[cas9]/(km+[ARG_2])
Through changing the copy numbers of two vectors in our system model, we could get a ratio of the copy numbers letting our system do nothing before we give the light signal, while having a higher reacting rate when we want it to work.
Result
Discussion
Our modeling and analysis focused on the aim of achieving a better theoretical ground to forecast how our system work after giving the light signal. From the test of ODE model of the light-controlled ARG cutting system ver3.0, we found that giving a short pulse light signal can make almost same effects as we constant light signal, so we find a plan to just give a short pulse light signal but make our system still response as fast as it was before, as well as saving energy used to give the light signal.
